MolNFT v1 · #142589 · protein
Complex of voltage-gated sodium channel navpas from american cockroach periplaneta americana bound with saxitoxin and DC1A
6A91 · Sodium channel protein PAFPC1: “Complex of voltage-gated sodium channel navpas from american cockroach periplaneta americana bound with…”. Electron microscopy, 3 ligands (PC1, 9SL, NAG), 20 pockets (best druggability 0.87). MolNFT…
- PDB
- 6A91
- Type
- protein
- Length
- 1,380 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein PAFPC1; Mu-diguetoxin-DC1A
- UniProt
- D0E0C2, P49126
- Ligands
- PC1, 9SL, NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein PAFPC1 | protein | 1323 | 61% helix, 2% strand | D0E0C2 |
| B | Mu-diguetoxin-DC1A | protein | 57 | 0% helix, 35% strand | P49126 |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains A, B
- 9SL · [(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,9,10-tetrahydro-3H,8H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.87 | 0.89 | 72 | 9SL |
| 2 | 513 | 0.69 | 0.79 | 44 | empty |
| 3 | 370 | 0.64 | 0.78 | 30 | empty |
| 4 | 236 | 0.61 | 0.81 | 35 | empty |
| 5 | 427 | 0.60 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1162 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 6A91 · Complex of voltage-gated sodium channel NavPaS from American cockroach Periplaneta… · the same entry in another collection · chain A against A, TM-score 1.00
- D0E0C2 · AlphaFold monomer V2.0 prediction for sodium channel protein PAFPC1 (D0E0C2) · a predicted model of the same protein · chain A against A, TM-score 0.93
- P49126 · AlphaFold monomer V2.0 prediction for beta-diguetoxin-DC1A (P49126) · a predicted model of the same protein · chain B against A, TM-score 0.91
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt D0E0C2
- Every structure of UniProt P49126
- Elsewhere: RCSB PDB 6A91 · PDBe 6A91 · UniProt D0E0C2 · UniProt P49126
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